TITLE: Ecommerce Tax Deadlines and Q4 Margin Checks: What to Review Now
This week, prepare for VAT and tax filing deadlines, review your Q4 marketplace margins and get your cross-border records in order. The dates and rules below reflect information available on 12 October 2026. Where a date or measure in an earlier brief needs clarification, we’ve noted it.
1. UK VAT: Prepare your 30 September return
Your VAT return and payment for the quarter ending 30 September 2026 are due by 7 November 2026. Reconcile your sales and VAT before submission so you can correct missing or duplicated entries in time.
For your ecommerce bookkeeping in the UK, check:
- Amazon settlement reports against your bookkeeping records, including refunds, fees and adjustments.
- Shopify orders against payout reports. Payouts may combine several orders and deduct fees.
- Gross sales, discounts, refunds and marketplace fees separately. A payout is not the same as taxable turnover.
- Marketplace-collected VAT. Identify VAT accounted for by a marketplace to avoid counting it twice.
- Stock locations and FBA fulfilment countries. Inventory held overseas may affect your VAT obligations there.
- Foreign-currency settlements and exchange rates. Keep records of the original currency, conversion and settlement amounts.
The UK VAT registration threshold is £90,000 of taxable turnover. Monitor your rolling 12-month total and the separate forward-look test, which can apply if you expect to exceed the threshold in the next 30 days. The deregistration threshold is £88,000, subject to HMRC’s conditions. See HMRC’s VAT threshold guidance.
2. Making Tax Digital for Income Tax: Submit your second update
If you have qualifying self-employment and property income over £50,000, the second quarterly update is due 7 November 2026. It covers the period from 6 July to 5 October, with figures reported cumulatively from 6 April.
MTD for Income Tax extends to qualifying income over £30,000 from 6 April 2027, then over £20,000 from April 2028. HMRC is not applying penalty points for late quarterly updates in 2026–27. That does not remove the requirement to submit updates, or the separate rules for late tax returns and payments. Check HMRC’s MTD guidance.
Limited companies are outside MTD for Income Tax. If you are a director with separate sole-trader selling activity, keep those records separate from your company’s books. Clear separation makes reporting easier and reduces the risk of mixing personal and company transactions.
3. Self Assessment: Fix a missed registration deadline
The 5 October 2026 registration deadline has passed for people who needed to file for the first time for 2025/26, including those with more than £1,000 of gross self-employment income.
If you missed it, register with HMRC as soon as possible. HMRC may issue a filing deadline based on when it contacts you, so follow the date in its notice. The usual online filing deadline for 2025/26 returns is 31 January 2027, and tax due is generally payable by then. Late filing, late-payment penalties and interest can apply. Starting now gives you more time to get your records together. See HMRC’s Self Assessment deadlines.
4. Q4 Amazon margins: Reforecast every unit
Amazon UK’s festive peak fulfilment fees apply to selected orders from 15 October 2026 to 14 January 2027. The announced average additions are around £0.12 per small or standard parcel item and £0.07 per large or extra-large envelope item. Oversize, Low-Price FBA and items delivered to buyers in other EU countries are excluded.
Amazon’s separate 1.5% fuel and logistics surcharge also applies to fulfilment fees. It is calculated on those fees, not on your selling price. Peak storage rates can increase for many categories; check the current rate card for your products rather than relying on a blanket estimate.
Amazon’s published Black Friday Week Prime-badge inbound dates were 21 October for European facilities and 28 October for UK facilities. Confirm product and account-specific requirements in Seller Central.
For Amazon FBA accounting in the UK, model each item’s referral fee, fulfilment and peak fees, fuel surcharge, storage, removals, promotions, VAT and settlement timing. A product can show a healthy sales forecast while cash margin shrinks after fees, promotions and delayed settlements.
5. Pricing and fee data: Reconcile on a fixed schedule
Seasonal deals and promotions can change the amount you actually receive per sale. Schedule a monthly fee reconciliation and compare expected charges with Amazon’s transaction, settlement and fee reports.
Investigate unexpected fulfilment, storage, removal or promotion charges in Seller Central. Where you identify eligible overcharges or lost inventory, submit the relevant claim and record any reimbursement or inventory adjustment in your books. A regular reconciliation helps prevent small discrepancies from accumulating through peak season.
6. US filings and imports: Check your records now
Foreign-owned US LLCs treated as disregarded entities, and certain foreign corporations with reportable transactions, may need to file Form 5472 with a pro forma Form 1120. For a calendar-year 2025 filer with a valid extension, 15 October 2026 is the final extended deadline. This is not a universal Form 5472 deadline; it depends on the filing entity and its return deadline.
A foreign-owned US disregarded entity cannot e-file Form 5472. IRS instructions permit fax or post for this filing. The IRS lists fax 855-887-7737 or mail to: Internal Revenue Service, 1973 Rulon White Blvd, M/S 6112, Attn: PIN Unit, Ogden, UT 84201. Missing or incomplete filings can trigger a $25,000 penalty per form, with further $25,000 penalties for each 30-day period the failure continues after IRS notice. If filing late, submit promptly and include a signed reasonable-cause statement explaining the circumstances and corrective steps. Review the IRS Form 5472 instructions.
For US importers of record, keep your physical address, email, telephone and EIN, SSN or CBP number accurate. Incomplete or inaccurate Form 5106 information can put your importer record at risk. Your customs broker’s Power of Attorney must be executed directly between you and the broker. See CBP’s Form 5106 guidance.
7. US sales tax and FIRPTA: Separate the obligations
Q4 order growth can push you over a state’s economic nexus threshold. Marketplace collection does not automatically remove your own registration, return or record-keeping obligations. FBA inventory in a state can also create physical nexus, depending on state rules.
Check state registration status, filing frequency and nexus tracking regularly. FIRPTA withholding relates to certain US real-property disposals by foreign persons; it is separate from sales tax and income tax reporting and should be handled under its own rules and timelines.
